title: RNA-seq of Molm13 cells with WT MGA C4

description:
SJ_MGA_human_RSEM_gene_count_final.txt
SJAML074858_C4_WT

data_processing:
RNA-Seq reads were mapped to GRCh38/hg38 human genome assembly using STAR v2.7.9a
Gene expression count matrix was generated using RSEM (v1.3.0)
The count data were transformed to log2-counts per million (log2CPM) using Voom method available from R package Limma (v3.50.3). Limma was also used to perform differential expression analysis between DMSO and dTAG-13 treated samples.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: tab-delimited text file for log2-counts per million (log2CPM) , one gene per row and one sample per column.
Supplementary files format and content: tab-delimited text file for gene counts , one gene per row and one sample per column.

extract_protocol:
RNA was extracted using a quick-RNA Microprep kit (Zymo Research, CA).
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599).


title: RNA-seq of Molm13 cells with WT MGA C3

status: Public on May 15 2024

type: SRA

city: Memphis

first: Michael

last: Walsh

address: 262 Danny Thomas

country: USA

institute: St Jude Children's Research Hospital

description:
SJ_MGA_human_RSEM_gene_count_final.txt
SJAML074858_C3_WT

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: AML

tag: genotype


title: GFP-LC3 oHSC_MID_89

city: New York

first: Paul

middle: Vincent

last: Dellorusso

state: NY

address: 701 West 168th Street, 724 Hammer Health Sciences Center

department: Genetics and Development

institute: Columbia University Irving Medical Center

description:
smartseq2
fcounts2.txt

library_source: transcriptomic single cell

data_processing:
scRNA-Seq reads were aligned to the mouse genome (mm10) with the STAR aligner (version 2.7.3a), sequences of eGFP and rat Map1lc3b were included in the index file, and subread featureCounts (version 2.0.0) function using the ENSEMBL v93 annotation.
Cells with >120,000 nuclear mapped reads, fraction of nuclear mapped reads mapped to genes >15% and fraction of mitochondrial reads relative to reads mapped to genes <20% were retained for downstream analysis.
Counts were normalised using size factor methods from DESeq2 and ERCCs were used to determine technical noise and highly variable genes.
Assembly: mouse
Supplementary files format and content: txt files containing raw fcount matrices

organism: Mus musculus

source_name: bone marrow

extract_protocol:
BM derived cells were isolated , crushed and filtered through 40µm nylon mesh. These cells were stained for surface markers and sorted . Single cells were individually sorted by fluorescence-activated cell sorting into 96-well PCR plates containing lysis buffer (10% Triton X-100, SUPERase-In RNase Inhibitor 20U/μl (Thermo Fisher Scientific) and DEPC-treated or Rnase-free H20), at 4°C.
Individual scRNA-seq libraries were prepared using a modified smartseq2 protocol (PMID: 30050112, PMID: 24385147 and PMID: 34057731).

tag: tissue

value: bone marrow

tag: age

value: old

value: Haematopoietic stem cell

tag: treatment

value: steady state isolation


title: 2294319_SJAML075820_C1-MOLM13_WT-IGG-AB14

library_source: genomic

data_processing:
To obtain quality reads, raw reads were processed and trimmed with Trim_galore (v0.4.4) from cutadapt (DOI: 10.14806ej.17.1.200) and FASTQC analysis. A default quality score cutoff of Q20 is used.  Quality trimmed reads were then mapped to "hg38+rDNA” (DOI: 10.1101/2022.11.10.514243) genome build by bwa (v0.7.12-r1039) and converted to a bam file by samtools (v1.2).
Duplicate reads were marked with biobambam2 (v2.0.87, DOI: 10.1186/175109473-9-13). Uniquely mapped and properly paired reads were then extracted with samtools (v1.2, "-F 1804 -q 1") and sorted by read name using biobambam2 (v2.0.87)
bedtools(v2.17.0, PMID: 20110278) were used to convert bam file to bedpe file as fragments. Fragments with size shorter than 2000bp were extracted and center 80bp of each fragment were used to generate bigwig track files by UCSC tools (v4) and visualized using IGV (v2.16.0).
Narrow peaks were called with MACS2 (v2.1.1.20160309, parameters "-q 0.05") and broad peaks were called by SICER (v1.1, parameters "hg38 1 200 fragmentsize 0.86 600 0.00001").
To perform statistical test between experimental groups, fragments for each reference peak were counted with intersect command from pybedtools (v0.9.1). Next, the number of raw reads mapping per peak were converted to FPKM unit (Fragments Per Kilo base per Million mapped reads), and TMM (trimmed mean of M-values) from edgeR package. Next, we used limma-voom approach to assess the significance of differential peak binding.  Significant peaks were defined by log2FC < -1 or > 1 and FDR < 0.05.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: BigWig format
Library strategy: CUT&RUN

molecule: genomic DNA

extract_protocol:
CUT&RUN was performed following the kit from EpiCypher (cat# 14-1048)
CUT&RUN DNA libraries were made following NEBNext Ultra II DNA Library Prep Kit for Illumina (cat# E7103), PCR amplification was done for 12 cycles

tag: chip antibody

value: anti-IgG, Epicypher 13-0042k


title: GFP-LC3 oHSC_LO_89

description:
smartseq2
fcounts2.txt


title: RNA-seq of Molm13 cells with WT MGA C2

description:
SJ_MGA_human_RSEM_gene_count_final.txt
SJAML074858_C2_WT


title: GFP-LC3 oHSC_HI_88

description:
smartseq2
fcounts2.txt


title: RNA-seq of Molm13 cells with homozygous deletion of MGA using CRISPR C4

description:
SJ_MGA_human_RSEM_gene_count_final.txt
SJAML074861_C4_Homo_Del


title: GFP-LC3 yHSC_88

description:
smartseq2
fcounts2.txt

value: young


title: GFP-LC3 yHSC_85

description:
smartseq2
fcounts2.txt


title: 2294324_SJAML075820_C2-MOLM13_KO-H3K4me3-AB12

value: anti-H3K4me3, Epicypher 13-0041


title: RNA-seq of Molm13 cells with homozygous deletion of MGA using CRISPR C2

description:
SJ_MGA_human_RSEM_gene_count_final.txt
SJAML074861_C2_Homo_Del


title: GFP-LC3 oHSC_HI_87

description:
smartseq2
fcounts2.txt


title: RNA-seq of Molm13 cells with homozygous deletion of MGA using CRISPR C3

description:
SJ_MGA_human_RSEM_gene_count_final.txt
SJAML074861_C3_Homo_Del


title: GFP-LC3 oHSC_MID_88

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_88

description:
smartseq2
fcounts2.txt


title: Mubritinib treated, biol rep 2, Hour 24

city: Pessac

first: Ahmad

last: Sharanek

address: Allée Geoffroy St Hilaire

country: France

institute: BRIC INSERM U1312

data_processing:
CBiB (Bordeaux Bioinformatics Center) standard pipeline for quality control, trimming, mapping and generation of raw counts matrix:  The 12 fastq files were received by the CBiB, Bordeaux, France for RNA-seq data analysis. Low quality reads trimming, and quality control, were carried out with fastp version 0.32.2 and MultiQC version 1.9, respectively. For mapping, STAR version 2.7.10a  was used, with the Gencode release 39 reference human genome. The count matrices were generated using the STAR output, retaining only uniquely mapped reads. Downstream analyses were performed in R version 4.1.0.
Quality control with MultiQC version 1.9.
Trimming of low quality reads, with fastp version 0.32.2
Mapping with STAR version 2.7.10a, with the Gencode release 39 reference human genome.
Generation of raw count matrices (only uniquely mapped reads) with R version 4.1.0 and the STAR output.
Assembly: Gencode release 39 reference of the human genome
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: BTSCs were cultured in low attachment flasks as spheres in DMEM/F12 media (Fisher Scientific, #11530566) supplemented with 2 mM GlutaMAX (ThermoFischer, #35050061), 1X B-27 supplement (ThermoFischer, #12587010), 2 μg/ml heparin (Sigma-Aldrich, #H3149), 20 ng/ml EGF (Peprotech, #AF-100-15), 20 ng/ml bFGF (Peprotech, #AF-100-18B), 100 U/ml penicillin-streptomycin (Fisher Scientific, #11548876). All cell lines were tested negative for mycoplasma. All cells were kept in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
Total RNA was extracted at LuxGen facility (Luxembourg Institute of Health) using Rneasy mini kit (Qiagen).  100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared at LuxGen facility, using the Illumina Stranded mRNA Ligation kit according to manufacturer.  All libraries have been quantified using a Qubit HS dsDNA kit (Thermofisher) and the library quality check has been performed using a High Sensitivity NGS Fragment Analysis Kit on a Fragment Analyzer System (Agilent Technologies). Indexed libraries were normalized and pooled to be sequenced on an Illumina  Novaseq 6000 sequencer according to manufacturer’s instructions with targeted conditions of 2 x 75bp and 25M reads/sample.

treatment_protocol: BTSC147 was treated with 500 nM of mubritinib for 24 h.

value: brain tumor stem cells

value: Mubritinib


title: GFP-LC3 yHSC_84

description:
smartseq2
fcounts2.txt


title: Mubritinib treated, biol rep 1, Hour 24


title: GFP-LC3 oHSC_MID_87

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_86

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_86

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_87

description:
smartseq2
fcounts2.txt


title: Control, biol rep 2, Hour 24

value: control


title: GFP-LC3 oHSC_HI_85

description:
smartseq2
fcounts2.txt


title: Control, biol rep 3, Hour 24


title: GFP-LC3 yHSC_83

description:
smartseq2
fcounts2.txt


title: Wt, INPUT, Rep1

city: Pittsburgh

first: Karen

last: Arndt

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Fastq files were demultiplexed and aligned to a hybrid K. lactis - S. cerevisiae genome using bowtie2
The resultant sam files were converted to bam and duplicates removed with Picard
Samtools counts of spike-in and sample and bam reads generated counts for Spike-in normalization factors using the inverse counts per-million method
Bam files were normalized and converted to bigwig using deeptools
Assembly: S. cerevisiae: Ensembl R64-3-1/K.lactis: ASM251v1 Hybrid Genome
Supplementary files format and content: spike-in normalized bigwig for IPs or unnormalized bigwigs for inputs

organism:
Saccharomyces cerevisiae
Kluyveromyces lactis

source_name: MATa his4-912δ lys2-128δ leu2Δ1 trp1Δ63 RPB3-3XFLAG::KANMX

growth_protocol: S. cerevisiae and S. pombe were grown in YPD standard rich growth medium supplemented with 400 μM tryptophan at 30°C.

extract_protocol:
Chromatin was fragmented using a Bioruptor® (Diagenode B01060010) with 25 cycles of 30 sec on and 30 sec off at 4°C.
Libraries were built using the NEBNext® Ultra™ II DNA Library Prep Kit (Illumina #E7645S/L) with 1.5 ng of immunoprecipitated or input DNA

treatment_protocol: Yeast cultures were grown to OD600 = 1-1.2 at 30°C. At the time of harvest, cells were fixed with 1% v/v formaldehyde for 20 min at room temperature after 30 min of treatment with 1:1000 v/v vehicle (DMSO) or auxin (final concentration of 500 μM in DMSO) if necessary. Fixation was quenched for 5 min with a 37.5 mL of 3M glycine and 20 mM Tris solution, the culture pelleted at 4,000 rpm at 4°C, and pellets were washed twice in TBS before snap freezing in liquid nitrogen.

tag: time (min)


title: Wt, antiFLAG, Rep2


title: GFP-LC3 oHSC_MID_86

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_86

description:
smartseq2
fcounts2.txt


title: Wt, INPUT, Rep2


title: GFP-LC3 yHSC_82

description:
smartseq2
fcounts2.txt


title: Control, biol rep 1, Hour 24


title: MDA-MB-453, shtRF, Day3, rep3

city: 南京市

first: xinyu

last: wan

state: 江苏省

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

country: China

institute: Nanjing medical university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of Homo sapiens from ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/ using STRA software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: excel file includes raw counts for each Sample
Supplementary files format and content: excel files include RPKM values for each Sample

growth_protocol: MDA-MB-453 cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in a humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit（Life Technologies，Q10210）.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: breast cancer cells

value: tRF-1-Ser knock down


title: GFP-LC3 oHSC_HI_84

description:
smartseq2
fcounts2.txt


title: ctr9D, INPUT, Rep2

source_name: MATα his4-912δ lys2-128δ leu2Δ1 trp1Δ63 RPB3-3XFLAG::KANMX ctr9∆::KANMX


title: MDA-MB-453, shtRF, Day3, rep2

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门


title: GFP-LC3 oHSC_MID_85

description:
smartseq2
fcounts2.txt


title: Mubritinib treated, biol rep 3, Hour 24


title: Wt, antiFLAG, Rep1


title: GFP-LC3 oHSC_HI_83

description:
smartseq2
fcounts2.txt


title: MDA-MB-453, shtRF, Day3, rep1

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门


title: GFP-LC3 oHSC_LO_85

description:
smartseq2
fcounts2.txt


title: ctr9D, INPUT, Rep1


title: GFP-LC3 yHSC_81

description:
smartseq2
fcounts2.txt


title: MDA-MB-453, Control, Day3, rep3

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

value: Control


title: GFP-LC3 yHSC_80

description:
smartseq2
fcounts2.txt


title: ctr9D, antiFLAG, Rep1


title: ctr9D, antiFLAG, Rep2


title: GFP-LC3 oHSC_MID_84

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_84

description:
smartseq2
fcounts2.txt


title: MDA-MB-453, Control, Day3, rep2

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门


title: GFP-LC3 oHSC_LO_83

description:
smartseq2
fcounts2.txt


title: MDA-MB-453, Control, Day3, rep1

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门


title: Ctr9, Veh, INPUT, Rep2

source_name: MATa his3Δ200::HIS3-osTIR lys2-128δ leu2Δ1 ura3-52 RPB3-3XFLAG::KANMX CTR9-V5-IAA7(AID)::KANMX


title: GFP-LC3 oHSC_MID_83

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_82

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_82

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_79

description:
smartseq2
fcounts2.txt


title: Ctr9, Veh, antiFLAG, Rep2


title: GFP-LC3 oHSC_HI_81

description:
smartseq2
fcounts2.txt


title: Ctr9, Veh, INPUT, Rep1


title: HEK293T siSERF2-2

city: Ann Arbor

first: James

middle: CA

last: Bardwell

state: Michigan

address: The University of Michigan Biological Sciences Building 1105 N University Ave

department: MCDB

institute: Univeristy of Michigan

description: HEK_siserf2VSHEK_sictrl_Gene_differential_expression.txt

data_processing:
Cutadapt was used to trim reads for adaptor contamination and low quality bases
Reads were mapped to hg38 with HISAT2 and assembled using StringTie
mRNA differential expression analysis was performed with DESeq2 using parameters FDR < 0.05 and absolute fold change >= 2
Assembly: hg38
Supplementary files format and content: text file of DESeq2 output with FPKM counts for each sample

growth_protocol: HeLa and HEK293T cells were grown in DMEM supplemented with 2mM glutamine, 10% fetal bovine serum, and 1X pencillin/streptomycin in a humidified atomosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen)
Poly(A) mRNA libraries for RNA-seq were prepared following Illumina's TruSeq-stranded-mRNA sample preparation protocol

treatment_protocol: Cells were reverse transfected with 25 nM of non-targeting control siRNA or siRNA targeting human ZNF706 or Serf2, then harvested ~48 hours post-transfection

value: embryonic kidney

value: siRNA knockdown of SERF2


title: HEK293T siSERF2-3


title: Ctr9, Veh, antiFLAG, Rep1


title: GFP-LC3 yHSC_78

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_81

description:
smartseq2
fcounts2.txt


title: HEK293T siSERF2-1


title: HeLa siSERF2-3

description: HeLa_siserf2VSHeLa_sictrl_Gene_differential_expression.txt

source_name: HeLa

value: HeLa

value: cervical cancer


title: Ctr9, Aux, INPUT, Rep2

value: 1:1000 v/v 0.5 M Auxin in DMSO


title: GFP-LC3 oHSC_MID_80

description:
smartseq2
fcounts2.txt

value: bone marrow

value: old


title: HeLa siSERF2-2


title: GFP-LC3 oHSC_LO_81

description:
smartseq2
fcounts2.txt

value: Haematopoietic stem cell

value: steady state isolation


title: HeLa siSERF2-1


title: GFP-LC3 yHSC_77

description:
smartseq2
fcounts2.txt

value: young


title: GFP-LC3 oHSC_HI_80

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_82

description:
smartseq2
fcounts2.txt


title: Ctr9, Aux, INPUT, Rep1


title: Ctr9, Aux, antiFLAG, Rep1


title: GFP-LC3 oHSC_HI_79

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_79

description:
smartseq2
fcounts2.txt


title: Ctr9, Aux, antiFLAG, Rep2


title: GFP-LC3 yHSC_76

description:
smartseq2
fcounts2.txt


title: 207854510042_R01C01

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.
Normalized average Beta

label: Cy5 and Cy3

source_name: Human cell line DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from 30-70 mg of tissue or 5.0 x 10^6 cells for cell lines using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol. DNA was quantified using a Qubit 4 Fluorometer (Invitrogen).

tag: modification


title: HEK293T siZNF706-3

description: HEK_siznf706VSHEK_sictrl_Gene_differential_expression.txt

value: siRNA knockdown of ZNF706


title: GFP-LC3 oHSC_LO_79

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_80

description:
smartseq2
fcounts2.txt


title: HEK293T siZNF706-2


title: GFP-LC3 oHSC_HI_78

description:
smartseq2
fcounts2.txt


title: 207760740083_R12C03

value: 50% EpigenDX


title: HEK293T siZNF706-1


title: GFP-LC3 oHSC_HI_77

description:
smartseq2
fcounts2.txt


title: 207854510042_R03C01


title: GFP-LC3 oHSC_MID_78

description:
smartseq2
fcounts2.txt


title: HEK293T siCTRL-3

value: siRNA knockdown control


title: GFP-LC3 oHSC_LO_78

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_76

description:
smartseq2
fcounts2.txt


title: 207760740030_R12C03


title: 207760740041_R12C03


title: HEK293T siCTRL-1


title: GFP-LC3 oHSC_MID_77

description:
smartseq2
fcounts2.txt


title: 207760740056_R12C03


title: HEK293T siCTRL-2


title: GFP-LC3 oHSC_LO_77

description:
smartseq2
fcounts2.txt


title: 207760740083_R08C03


title: GFP-LC3 oHSC_MID_76

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_73

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_75

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_72

description:
smartseq2
fcounts2.txt


title: HeLa siZNF706-2

description: HeLa_siznf706VSHeLa_sictrl_Gene_differential_expression.txt


title: 207760740083_R06C03


title: 207760740083_R02C03


title: GFP-LC3 yHSC_75

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_76

description:
smartseq2
fcounts2.txt


title: HeLa siZNF706-1


title: GFP-LC3 oHSC_HI_74

description:
smartseq2
fcounts2.txt


title: 207760740083_R04C03


title: GFP-LC3 oHSC_MID_75

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_75

description:
smartseq2
fcounts2.txt


title: HeLa siCTRL-3


title: GFP-LC3 yHSC_74

description:
smartseq2
fcounts2.txt


title: HeLa siCTRL-2


title: GFP-LC3 oHSC_HI_73

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_74

description:
smartseq2
fcounts2.txt


title: 207760740056_R06C03


title: HeLa siZNF706-3


title: 207760740056_R04C03


title: GFP-LC3 oHSC_LO_74

description:
smartseq2
fcounts2.txt


title: HeLa siCTRL-1


title: CAL27/OXA-1

city: Fuzhou

first: Kairui

last: Sun

state: Fujian

address: Jiaotong Road 88

department: School and Hospital of Stomatology

institute: Fujian Medical University

data_processing:
Casava 1.8
Sequence reads were trimmed for adapter sequence/low-quality sequence using Illumina Casava 1.8.
Trimmed sequence reads were mapped to the reference genome GRCh38/hg38 using Hisat2 v2.0.5.
Read count extraction and normalization were performed using Illumina Casava 1.8.
Assembly: hg38
Supplementary files format and content: Please note that two processed data column was generated from each sample (one from R1 and the other from R2 mate file of paired-end files)

growth_protocol: The human OSCC cell line CAL27 and the corresponding 5FU-resistant and OXA-resistant cells were maintained in high-glucose DMEM supplemented with 10% fetal bovine serum (FBS) at 37℃ in humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations and construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacture's protocols.

treatment_protocol: The parental CAL27 cells were maintained in drug-free medium. The 5FU-resistant cells were maintained in medium supplemented with 10μM 5FU and the OXA-resistant cells were maintained in medium supplemented with 10μM OXA.

value: Oral squamouscarcinoma cell line

value: oxaliplatin resistant

value: 10μM OXA


title: GFP-LC3 yHSC_70

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_73

description:
smartseq2
fcounts2.txt


title: 207760740056_R02C03


title: GFP-LC3 yHSC_71

description:
smartseq2
fcounts2.txt


title: CAL27/5FU-1

value: 5-fluorouracil resistant

value: 10μM 5FU


title: GFP-LC3 oHSC_HI_72

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_71

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_72

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_73

description:
smartseq2
fcounts2.txt


title: CAL27-1

value: WT

value: drug-free


title: 207760740041_R06C03


title: MDA-MB-453, 25(OH)D, Day5, rep2

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

growth_protocol: MDA-MB-453 cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 in 37℃.

extract_protocol:
Total RNA was extracted using TRIzol reagant(Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit（Life Technologies，Q10210）.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: breast cancer cells


title: GFP-LC3 yHSC_68

description:
smartseq2
fcounts1.txt


title: 207760740056_R08C03


title: 207760740041_R08C03


title: MDA-MB-453, 25(OH)D, Day5, rep3

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门


title: GFP-LC3 oHSC_MID_71

description:
smartseq2
fcounts1.txt


title: 207760740041_R02C03


title: MDA-MB-453, 25(OH)D, Day5, rep1

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门


title: GFP-LC3 yHSC_69

description:
smartseq2
fcounts2.txt


title: 207760740030_R08C03


title: GFP-LC3 yHSC_67

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_71

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_69

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_70

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_66

description:
smartseq2
fcounts1.txt


title: MDA-MB-453, Control, Day5, rep3

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

value: solvent


title: GFP-LC3 oHSC_MID_69

description:
smartseq2
fcounts1.txt

value: bone marrow


title: 207760740030_R04C03


title: GFP-LC3 oHSC_HI_68

description:
smartseq2
fcounts1.txt

value: old


title: GFP-LC3 oHSC_LO_70

description:
smartseq2
fcounts1.txt

value: Haematopoietic stem cell


title: 207760740030_R06C03


title: MDA-MB-453, Control, Day5, rep2

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门


title: GFP-LC3 oHSC_HI_70

description:
smartseq2
fcounts1.txt

value: steady state isolation


title: GFP-LC3 oHSC_LO_72

description:
smartseq2
fcounts1.txt


title: Human_ONB_B

city: Durham

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

state: NC

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

description: 10X Genomic 3' GEX

data_processing:
Demulitplexed with 10x cellranger mkfastq to create fastq files with sample index (I1, I2) and read files (R1, R2).
Reads were aligned to the human genome (refdata-cellranger-GRCh38) from 10X Genomics and count barcodes and UMIs were generated using cellranger count v7.1.0 .
Downstream visualization and further analysis of scRNA seq data was performed in R with Seurat and/or Python with Scanpy.
Assembly: Human (GRCh38) 2020-A-2.0.0
Supplementary files format and content: Filtered feature-barcode matrices  from cellranger count.

source_name: tumor cells

extract_protocol:
Each tumor sample was subject to enzymatic/mechanical digestion into a single nucleus suspension. 10x Genomics gel beads and reverse transcription reagents were added to cell suspensions and loaded to a chromium single cell controller to form gel-bead-in emulsions (GEMs). From GEMs, cDNA was generated from barcoded mRNA and subsequent A tailing, end repair, adaptor ligation, and sample indexing was performed according to manufacturer. Libraries were assessed on Agilent D5000 ScreenTape on an Agilent Tech 2200 tapestation system and quantified by Kapa Biosystems Library Quantification Kit for Illumina Platforms. Libraries were sequenced on the Novaseq 6000 w 2x150 paired end seq targeting ~30k reads/cell.
10X Genomics Single-Cell 3' RNA Dual Index v3

value: tumor cells


title: 207760740030_R02C03


title: GFP-LC3 oHSC_LO_69

description:
smartseq2
fcounts1.txt


title: MDA-MB-453, Control, Day5, rep1

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门


title: GFP-LC3 yHSC_65

description:
smartseq2
fcounts1.txt

value: young


title: 207760740041_R04C03


title: GFP-LC3 oHSC_MID_68

description:
smartseq2
fcounts1.txt


title: SKOV-3, SIVA-D160N transfection

city: Portland

first: Shiuh-Wen

last: Luoh

state: OR

address: 3181 SW Sam Jackson Park Rd

department: MMG

institute: Oregon Health & Science University

description:
SKOV3pm
cpm_values.tsv
rpkm_values.tsv

data_processing:
Sequencing/Base calling: NovaSeq 6000 with RTA3
QC: FastQC
Alignment: STAR_2.5.3a
Processing: TMM normalization in edgeR Bioconductor package with conversion to counts per million (CPM)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file of raw read counts for all samples
Supplementary files format and content: Tab-delimited text file of CPM values for all samples; non-expressing genes removed

source_name: ovarian

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with 10% FBS. Passaging/harvesting carried out at 80% confluence in a 37C, 5% CO2 environment.

extract_protocol:
Trizol
Illumina TruSeq Stranded mRNA Kit

treatment_protocol: Lipofectamine 3000 Transfection Reagent used for transfection of 1ug SspI-linearized vector according to manufacturer's instructions. After 24h, cells were selected with 0.8mg/mL hygromycin.

value: ovarian

value: SIVA-D160N transfection


title: GFP-LC3 oHSC_HI_67

description:
smartseq2
fcounts1.txt


title: 207760740083_R15C03


title: GFP-LC3 oHSC_LO_68

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_64

description:
smartseq2
fcounts1.txt


title: 207760740083_R11C03


title: SKOV-3, parental

description:
SKOV3ctrol
cpm_values.tsv
rpkm_values.tsv


title: GFP-LC3 oHSC_HI_66

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_67

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_67

description:
smartseq2
fcounts1.txt


title: OVAR-8, SIVA-WT transfection

description:
OVCAR8wt
cpm_values.tsv
rpkm_values.tsv

value: SIVA-WT transfection


title: OVAR-8, SIVA-D160N transfection

description:
OVCAR8pm
cpm_values.tsv
rpkm_values.tsv


title: GFP-LC3 oHSC_HI_65

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_66

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_66

description:
smartseq2
fcounts1.txt


title: 207760740083_R09C03


title: 207760740056_R15C03


title: HCC1954, SIVA-D160N transfection

description:
HCCpm
cpm_values.tsv
rpkm_values.tsv

source_name: breast

value: breast


title: 207760740056_R13C03


title: OVAR-8, parental

description:
OVCAR8ctrol
cpm_values.tsv
rpkm_values.tsv


title: HCC1954, SIVA-WT transfection

description:
HCCwt
cpm_values.tsv
rpkm_values.tsv


title: 207760740056_R09C03


title: GFP-LC3 oHSC_HI_64

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_65

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_65

description:
smartseq2
fcounts1.txt


title: HCC1954, parental

description:
HCCctrol
cpm_values.tsv
rpkm_values.tsv


title: GFP-LC3 yHSC_61

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_63

description:
smartseq2
fcounts1.txt


title: SKOV-3, SIVA-WT transfection

description:
SKOV3wt
cpm_values.tsv
rpkm_values.tsv


title: 207760740041_R15C03


title: GFP-LC3 yHSC_63

description:
smartseq2
fcounts1.txt


title: 207760740083_R13C03


title: GFP-LC3 yHSC_62

description:
smartseq2
fcounts1.txt


title: MDA-MB-231, SIVA-D160N transfection

description:
x231pm
cpm_values.tsv
rpkm_values.tsv


title: 207760740041_R13C03


title: GFP-LC3 yHSC_60

description:
smartseq2
fcounts1.txt


title: 207760740041_R11C03


title: GFP-LC3 oHSC_MID_63

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_62

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_63

description:
smartseq2
fcounts1.txt


title: 207760740041_R09C03


title: MDA-MB-231, parental

description:
x231ctrol
cpm_values.tsv
rpkm_values.tsv


title: GFP-LC3 oHSC_HI_61

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_62

description:
smartseq2
fcounts1.txt


title: 207760740030_R13C03


title: GFP-LC3 oHSC_LO_62

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_60

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_58

description:
smartseq2
fcounts1.txt


title: 3.16uM_Prochloraz_MCF7, M_397

first: Rasim

last: Barutcu

address: 6 Davis Drive

institute: ScitoVation

description:
M_397
MCF7_Prochloraz_3.16uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

data_processing:
Reads were mapped to the Ensembl human reference genome (hg38) using HISAT2 (version 2.05) (Zhang et al. 2021).
Alternative splicing analysis of RNA-Seq data was performed with vast-tools version 2 (Tapial et al. 2017). The INCLUSION files xontain information about the quality and raw percent spliced-in (PSI) values of each replicate. The headers of the INCLUSION files contain the cell type, the chemical, the dose, and the replicate number separated by underscores '_'. More information about this file type ccan be found at: https://github.com/vastgroup/vast-tools
Assembly: hg38
Supplementary files format and content: Read count table
Supplementary files format and content: Metadata table
Supplementary files format and content: Splicing inclusion files showing the raw percent spliced-in (PSI) values

growth_protocol: A549 cells were obtained from the American Type Culture Collection (ATCC). Proliferation media consisted of Dulbecco’s Modified Essential Medium (Gibco) with 10% FBS (Atlanta Biologicals) and 1% penicillin-streptomycin (Gibco). The plating medium consisted of Dulbecco’s Modified Essential Medium (Gibco) with 10% Heat-Inactivated FBS (HI FBS; Atlanta Biologicals) and 1% penicillin-streptomycin (Gibco). For passaging, cells were washed with sterile DPBS and enzymatically removed using 0.25% trypsin-EDTA (Gibco). In preparation for the proliferation assay, A549 cells were thawed (2.0 x 106, passage 3) and placed into a T25 flask (CytoOne; USA Scientific, Ocala, FL). After 5 days in culture, cells were passaged into a T75 flask (2.0 x 106, passage 4) using a plating medium (10% HI FBS). After 5 days, cells were plated at a density of 35,000 cells/well in black-walled, clear-bottom, tissue-culture-treated 96-well plates (Greiner Bio-One) using a plating medium (10% HI FBS). Cells were cultured for 48 h in 96-well plates prior to treatment.

extract_protocol:
Nextera XT DNA Library Preparation Kit
polyA enrichment
Illumina 150bp paired-end reads

value: tumorigenic breast epithelial cell

value: MCF7 cells treated with 3.16uM Prochloraz


title: 10uM_Prochloraz_MCF7, M_398

description:
M_398
MCF7_Prochloraz_10uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 10uM Prochloraz


title: 31.6uM_Prochloraz_MCF7, M_399

description:
M_399
MCF7_Prochloraz_31.6uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 31.6uM Prochloraz


title: 207760740030_R11C03


title: GFP-LC3 oHSC_LO_61

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_61

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_59

description:
smartseq2
fcounts1.txt


title: 207760740083_R07C03


title: GFP-LC3 yHSC_57

description:
smartseq2
fcounts1.txt


title: 100uM_Prochloraz_MCF7, M_395

description:
M_395
MCF7_Prochloraz_100uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 100uM Prochloraz


title: 1uM_Prochloraz_MCF7, M_396

description:
M_396
MCF7_Prochloraz_1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 1uM Prochloraz


title: GFP-LC3 oHSC_MID_60

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_59

description:
smartseq2
fcounts1.txt


title: 207760740030_R15C03


title: 207760740083_R05C03


title: GFP-LC3 oHSC_LO_60

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_56

description:
smartseq2
fcounts1.txt


title: 207760740030_R09C03


title: GFP-LC3 oHSC_MID_64

description:
smartseq2
fcounts1.txt


title: 100uM_Prochloraz_MCF7, M_400

description:
M_400
MCF7_Prochloraz_100uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: MDA-MB-231, SIVA-WT transfection

description:
x231wt
cpm_values.tsv
rpkm_values.tsv


title: GFP-LC3 oHSC_MID_59

description:
smartseq2
fcounts1.txt


title: 10uM_Prochloraz_MCF7, M_393

description:
M_393
MCF7_Prochloraz_10uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 yHSC_55

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_59

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_58

description:
smartseq2
fcounts1.txt


title: 1uM_Prochloraz_MCF7, M_391

description:
M_391
MCF7_Prochloraz_1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740083_R01C03


title: 207760740056_R07C03


title: 3.16uM_Prochloraz_MCF7, M_392

description:
M_392
MCF7_Prochloraz_3.16uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740056_R05C03


title: 207760740056_R11C03


title: GFP-LC3 oHSC_LO_64

description:
smartseq2
fcounts1.txt


title: 31.6uM_Prochloraz_MCF7, M_394

description:
M_394
MCF7_Prochloraz_31.6uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 yHSC_54

description:
smartseq2
fcounts1.txt


title: 207760740056_R03C03


title: 207760740056_R01C03


title: 207760740083_R03C03


title: GFP-LC3 oHSC_LO_57

description:
smartseq2
fcounts1.txt


title: 10uM_Prochloraz_MCF7, M_388

description:
M_388
MCF7_Prochloraz_10uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_57

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_53

description:
smartseq2
fcounts1.txt


title: 31.6uM_Prochloraz_MCF7, M_389

description:
M_389
MCF7_Prochloraz_31.6uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_55

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_56

description:
smartseq2
fcounts1.txt


title: 207760740041_R07C03


title: GFP-LC3 oHSC_HI_57

description:
smartseq2
fcounts1.txt


title: 3.16uM_Prochloraz_MCF7, M_387

description:
M_387
MCF7_Prochloraz_3.16uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_58

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_56

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_52

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_54

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_58

description:
smartseq2
fcounts1.txt


title: 1uM_Prochloraz_MCF7, M_386

description:
M_386
MCF7_Prochloraz_1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R03C03


title: GFP-LC3 oHSC_MID_55

description:
smartseq2
fcounts1.txt


title: 207760740041_R05C03


title: 207760740041_R01C03


title: GFP-LC3 oHSC_LO_55

description:
smartseq2
fcounts1.txt


title: 100uM_Prochloraz_MCF7, M_390

description:
M_390
MCF7_Prochloraz_100uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 yHSC_51

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_56

description:
smartseq2
fcounts1.txt


title: 31.6uM_Prochloraz_MCF7, M_384

description:
M_384
MCF7_Prochloraz_31.6uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_53

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_50

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_54

description:
smartseq2
fcounts1.txt


title: 10uM_Prochloraz_MCF7, M_383

description:
M_383
MCF7_Prochloraz_10uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_52

description:
smartseq2
fcounts1.txt


title: 207760740030_R03C03


title: 207760740030_R05C03


title: GFP-LC3 oHSC_MID_53

description:
smartseq2
fcounts1.txt


title: 1uM_Prochloraz_MCF7, M_381

description:
M_381
MCF7_Prochloraz_1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740030_R01C03


title: GFP-LC3 yHSC_49

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_53

description:
smartseq2
fcounts1.txt


title: 207760740083_R16C02


title: 100uM_Prochloraz_MCF7, M_385

description:
M_385
MCF7_Prochloraz_100uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_52

description:
smartseq2
fcounts1.txt


title: 0.316uM_Prochloraz_MCF7, M_380

description:
M_380
MCF7_Prochloraz_0.316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.316uM Prochloraz


title: 0.1uM_Prochloraz_MCF7, M_379

description:
M_379
MCF7_Prochloraz_0.1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.1uM Prochloraz


title: GFP-LC3 oHSC_HI_50

description:
smartseq2
fcounts1.txt

value: bone marrow

value: old


title: 0.0316uM_Prochloraz_MCF7, M_378

description:
M_378
MCF7_Prochloraz_0.0316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.0316uM Prochloraz


title: GFP-LC3 oHSC_MID_51

description:
smartseq2
fcounts1.txt

value: Haematopoietic stem cell

value: steady state isolation


title: 207760740030_R07C03


title: 207760740083_R14C02


title: 207760740083_R12C02


title: GFP-LC3 oHSC_LO_51

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_52

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_48

description:
smartseq2
fcounts1.txt

value: young


title: 207760740083_R10C02


title: 0.01uM_Prochloraz_MCF7, M_377

description:
M_377
MCF7_Prochloraz_0.01uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.01uM Prochloraz


title: 3.16uM_Prochloraz_MCF7, M_382

description:
M_382
MCF7_Prochloraz_3.16uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740056_R16C02


title: GFP-LC3 oHSC_HI_49

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_50

description:
smartseq2
fcounts1.txt


title: 0uM_Prochloraz_MCF7, M_376

description:
M_376
MCF7_Prochloraz_0uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0uM Prochloraz


title: GFP-LC3 oHSC_MID_54

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_47

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_50

description:
smartseq2
fcounts1.txt


title: 207760740056_R14C02


title: 0.316uM_Prochloraz_MCF7, M_375

description:
M_375
MCF7_Prochloraz_0.316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_48

description:
smartseq2
fcounts1.txt


title: 0.1uM_Prochloraz_MCF7, M_374

description:
M_374
MCF7_Prochloraz_0.1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_51

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_49

description:
smartseq2
fcounts1.txt


title: 207760740056_R12C02


title: GFP-LC3 oHSC_LO_49

description:
smartseq2
fcounts1.txt


title: 0.0316uM_Prochloraz_MCF7, M_373

description:
M_373
MCF7_Prochloraz_0.0316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_47

description:
smartseq2
fcounts1.txt


title: 207760740056_R10C02


title: 0.01uM_Prochloraz_MCF7, M_372

description:
M_372
MCF7_Prochloraz_0.01uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R14C02


title: GFP-LC3 oHSC_LO_48

description:
smartseq2
fcounts1.txt


title: 0uM_Prochloraz_MCF7, M_371

description:
M_371
MCF7_Prochloraz_0uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R16C02


title: GFP-LC3 yHSC_45

description:
smartseq2
fcounts1.txt


title: 0.316uM_Prochloraz_MCF7, M_370

description:
M_370
MCF7_Prochloraz_0.316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R12C02


title: GFP-LC3 oHSC_HI_46

description:
smartseq2
fcounts1.txt


title: 207760740041_R10C02


title: GFP-LC3 yHSC_44

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_47

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_45

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_47

description:
smartseq2
fcounts1.txt


title: 207760740030_R14C02


title: 0.01uM_Prochloraz_MCF7, M_367

description:
M_367
MCF7_Prochloraz_0.01uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_44

description:
smartseq2
fcounts1.txt


title: 0.1uM_Prochloraz_MCF7, M_369

description:
M_369
MCF7_Prochloraz_0.1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 yHSC_46

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_43

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_46

description:
smartseq2
fcounts1.txt


title: 0uM_Prochloraz_MCF7, M_366

description:
M_366
MCF7_Prochloraz_0uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_46

description:
smartseq2
fcounts1.txt


title: 207760740030_R16C02


title: GFP-LC3 oHSC_MID_45

description:
smartseq2
fcounts1.txt


title: 207760740030_R12C02


title: 207760740030_R10C02


title: 0.316uM_Prochloraz_MCF7, M_365

description:
M_365
MCF7_Prochloraz_0.316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 yHSC_42

description:
smartseq2
fcounts1.txt


title: 207760740083_R08C02


title: GFP-LC3 oHSC_MID_48

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_44

description:
smartseq2
fcounts1.txt


title: 0.0316uM_Prochloraz_MCF7, M_368

description:
M_368
MCF7_Prochloraz_0.0316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_LO_45

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_43

description:
smartseq2
fcounts1.txt


title: 0.1uM_Prochloraz_MCF7, M_364

description:
M_364
MCF7_Prochloraz_0.1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_44

description:
smartseq2
fcounts1.txt


title: 0.01uM_Prochloraz_MCF7, M_362

description:
M_362
MCF7_Prochloraz_0.01uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_42

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_43

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_41

description:
smartseq2
fcounts1.txt


title: 0.0316uM_Prochloraz_MCF7, M_363

description:
M_363
MCF7_Prochloraz_0.0316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740083_R06C02


title: 207760740083_R04C02


title: 10uM_DNCB_MCF7, M_360

description:
M_360
MCF7_DNCB_10uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 10uM DNCB


title: 3.16uM_DNCB_MCF7, M_359

description:
M_359
MCF7_DNCB_3.16uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell

value: MCF7 cells treated with 3.16uM DNCB


title: GFP-LC3 oHSC_LO_43

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_41

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_41

description:
smartseq2
fcounts1.txt


title: 0uM_Prochloraz_MCF7, M_361

description:
M_361
MCF7_Prochloraz_0uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_MCF7.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_42

description:
smartseq2
fcounts1.txt


title: 207760740056_R08C02


title: 207760740083_R02C02


title: 1uM_DNCB_MCF7, M_358

description:
M_358
MCF7_DNCB_1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 1uM DNCB


title: 207760740056_R04C02


title: GFP-LC3 yHSC_40

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_42

description:
smartseq2
fcounts1.txt


title: 207760740056_R02C02


title: 0.316uM_DNCB_MCF7, M_357

description:
M_357
MCF7_DNCB_0.316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.316uM DNCB


title: GFP-LC3 oHSC_HI_40

description:
smartseq2
fcounts1.txt


title: 0.1uM_DNCB_MCF7, M_356

description:
M_356
MCF7_DNCB_0.1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.1uM DNCB


title: GFP-LC3 oHSC_LO_41

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_39

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_40

description:
smartseq2
fcounts1.txt


title: 207760740056_R06C02


title: GFP-LC3 oHSC_MID_39

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_39

description:
smartseq2
fcounts1.txt


title: 207760740041_R08C02


title: 207760740041_R06C02


title: 10uM_DNCB_MCF7, M_355

description:
M_355
MCF7_DNCB_10uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_38

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_40

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_38

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_39

description:
smartseq2
fcounts1.txt


title: 3.16uM_DNCB_MCF7, M_354

description:
M_354
MCF7_DNCB_3.16uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R04C02


title: GFP-LC3 oHSC_HI_37

description:
smartseq2
fcounts1.txt


title: 207760740041_R02C02


title: GFP-LC3 oHSC_LO_38

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_38

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_37

description:
smartseq2
fcounts1.txt


title: 0.316uM_DNCB_MCF7, M_352

description:
M_352
MCF7_DNCB_0.316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0.1uM_DNCB_MCF7, M_351

description:
M_351
MCF7_DNCB_0.1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_37

description:
smartseq2
fcounts1.txt


title: 207760740030_R08C02


title: GFP-LC3 oHSC_LO_37

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_36

description:
smartseq2
fcounts1.txt


title: 207760740030_R04C02


title: GFP-LC3 yHSC_36

description:
smartseq2
fcounts1.txt


title: 3.16uM_DNCB_MCF7, M_349

description:
M_349
MCF7_DNCB_3.16uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 10uM_DNCB_MCF7, M_350

description:
M_350
MCF7_DNCB_10uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740030_R02C02


title: GFP-LC3 oHSC_MID_36

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_36

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_34

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_35

description:
smartseq2
fcounts1.txt


title: 1uM_DNCB_MCF7, M_348

description:
M_348
MCF7_DNCB_1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0.316uM_DNCB_MCF7, M_347

description:
M_347
MCF7_DNCB_0.316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_35

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_35

description:
smartseq2
fcounts1.txt


title: 207760740083_R15C02


title: 0.1uM_DNCB_MCF7, M_346

description:
M_346
MCF7_DNCB_0.1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 1uM_DNCB_MCF7, M_353

description:
M_353
MCF7_DNCB_1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 yHSC_34

description:
smartseq2
fcounts1.txt


title: 207760740083_R11C02


title: GFP-LC3 oHSC_HI_33

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_35

description:
smartseq2
fcounts1.txt


title: 207760740030_R06C02


title: 10uM_DNCB_MCF7, M_345

description:
M_345
MCF7_DNCB_10uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740083_R09C02


title: GFP-LC3 oHSC_MID_34

description:
smartseq2
fcounts1.txt


title: 3.16uM_DNCB_MCF7, M_344

description:
M_344
MCF7_DNCB_3.16uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_LO_34

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_32

description:
smartseq2
fcounts1.txt


title: 207760740056_R15C02


title: GFP-LC3 yHSC_33

description:
smartseq2
fcounts1.txt


title: 207760740083_R13C02


title: GFP-LC3 oHSC_MID_33

description:
smartseq2
fcounts1.txt


title: 0.316uM_DNCB_MCF7, M_342

description:
M_342
MCF7_DNCB_0.316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740056_R11C02


title: GFP-LC3 oHSC_HI_31

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_32

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_32

description:
smartseq2
fcounts1.txt


title: 207760740056_R09C02


title: 0.0316uM_DNCB_MCF7, M_340

description:
M_340
MCF7_DNCB_0.0316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.0316uM DNCB


title: GFP-LC3 oHSC_MID_32

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_33

description:
smartseq2
fcounts1.txt


title: 0.1uM_DNCB_MCF7, M_341

description:
M_341
MCF7_DNCB_0.1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R15C02


title: GFP-LC3 yHSC_31

description:
smartseq2
fcounts1.txt


title: 207760740041_R13C02


title: GFP-LC3 oHSC_HI_30

description:
smartseq2
fcounts1.txt


title: 0.00316uM_DNCB_MCF7, M_338

description:
M_338
MCF7_DNCB_0.00316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.00316uM DNCB


title: 0.01uM_DNCB_MCF7, M_339

description:
M_339
MCF7_DNCB_0.01uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.01uM DNCB


title: GFP-LC3 oHSC_HI_29

description:
smartseq2
fcounts1.txt

value: bone marrow


title: 207760740041_R11C02


title: GFP-LC3 yHSC_30

description:
smartseq2
fcounts1.txt


title: 207760740041_R09C02


title: GFP-LC3 oHSC_LO_31

description:
smartseq2
fcounts1.txt

value: old


title: 207760740056_R13C02


title: 0.001uM_DNCB_MCF7, M_337

description:
M_337
MCF7_DNCB_0.001uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.001uM DNCB


title: 1uM_DNCB_MCF7, M_343

description:
M_343
MCF7_DNCB_1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740030_R15C02


title: GFP-LC3 yHSC_29

description:
smartseq2
fcounts1.txt

value: Haematopoietic stem cell


title: GFP-LC3 oHSC_HI_28

description:
smartseq2
fcounts1.txt

value: steady state isolation


title: 0.0316uM_DNCB_MCF7, M_335

description:
M_335
MCF7_DNCB_0.0316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_29

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_29

description:
smartseq2
fcounts1.txt


title: 207760740030_R11C02


title: GFP-LC3 yHSC_28

description:
smartseq2
fcounts1.txt

value: young


title: 207760740030_R13C02


title: 0.01uM_DNCB_MCF7, M_334

description:
M_334
MCF7_DNCB_0.01uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_31

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_27

description:
smartseq2
fcounts1.txt


title: 207760740030_R09C02


title: GFP-LC3 oHSC_LO_28

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_27

description:
smartseq2
fcounts1.txt


title: 0.001uM_DNCB_MCF7, M_332

description:
M_332
MCF7_DNCB_0.001uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_30

description:
smartseq2
fcounts1.txt


title: 207760740083_R16C01

value: Raji


title: GFP-LC3 oHSC_LO_27

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_30

description:
smartseq2
fcounts1.txt


title: 0.00316uM_DNCB_MCF7, M_333

description:
M_333
MCF7_DNCB_0.00316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_26

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_27

description:
smartseq2
fcounts1.txt


title: 0uM_DNCB_MCF7, M_336

description:
M_336
MCF7_DNCB_0uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0uM DNCB


title: GFP-LC3 oHSC_MID_26

description:
smartseq2
fcounts1.txt


title: 207760740083_R12C01


title: 0.0316uM_DNCB_MCF7, M_330

description:
M_330
MCF7_DNCB_0.0316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_LO_26

description:
smartseq2
fcounts1.txt


title: 0.01uM_DNCB_MCF7, M_329

description:
M_329
MCF7_DNCB_0.01uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 yHSC_26

description:
smartseq2
fcounts1.txt


title: 207760740083_R10C01


title: GFP-LC3 oHSC_HI_25

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_28

description:
smartseq2
fcounts1.txt


title: 207760740056_R16C01


title: GFP-LC3 oHSC_MID_25

description:
smartseq2
fcounts1.txt


title: 0.00316uM_DNCB_MCF7, M_328

description:
M_328
MCF7_DNCB_0.00316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0.001uM_DNCB_MCF7, M_327

description:
M_327
MCF7_DNCB_0.001uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740056_R14C01


title: GFP-LC3 oHSC_LO_25

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_24

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_25

description:
smartseq2
fcounts1.txt


title: 207760740083_R14C01


title: 207760740056_R12C01


title: 0uM_DNCB_MCF7, M_331

description:
M_331
MCF7_DNCB_0uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0uM_DNCB_MCF7, M_326

description:
M_326
MCF7_DNCB_0uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_24

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_24

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_24

description:
smartseq2
fcounts1.txt


title: 0.0316uM_DNCB_MCF7, M_325

description:
M_325
MCF7_DNCB_0.0316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740056_R10C01


title: GFP-LC3 oHSC_HI_23

description:
smartseq2
fcounts1.txt


title: 0.01uM_DNCB_MCF7, M_324

description:
M_324
MCF7_DNCB_0.01uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_23

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_23

description:
smartseq2
fcounts1.txt


title: 0.00316uM_DNCB_MCF7, M_323

description:
M_323
MCF7_DNCB_0.00316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R14C01


title: GFP-LC3 oHSC_HI_22

description:
smartseq2
fcounts1.txt


title: 207760740041_R16C01


title: 207760740041_R12C01


title: GFP-LC3 oHSC_MID_22

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_22

description:
smartseq2
fcounts1.txt


title: 1mM_Diazinon_MCF7, M_320

description:
M_320
MCF7_Diazinon_1mM_Rep4
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 1mM Diazinon


title: 207760740030_R16C01


title: 0uM_DNCB_MCF7, M_321

description:
M_321
MCF7_DNCB_0uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell


title: GFP-LC3 oHSC_LO_22

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_21

description:
smartseq2
fcounts1.txt


title: 207760740041_R10C01


title: GFP-LC3 oHSC_HI_21

description:
smartseq2
fcounts1.txt


title: 0.001uM_DNCB_MCF7, M_322

description:
M_322
MCF7_DNCB_0.001uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_LO_21

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_20

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_20

description:
smartseq2
fcounts1.txt


title: 207760740030_R14C01


title: 316uM_Diazinon_MCF7, M_319

description:
M_319
MCF7_Diazinon_316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 316uM Diazinon


title: GFP-LC3 yHSC_21

description:
smartseq2
fcounts1.txt


title: 100uM_Diazinon_MCF7, M_318

description:
M_318
MCF7_Diazinon_100uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 100uM Diazinon


title: GFP-LC3 yHSC_20

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_20

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_19

description:
smartseq2
fcounts1.txt


title: 31.6uM_Diazinon_MCF7, M_317

description:
M_317
MCF7_Diazinon_31.6uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 31.6uM Diazinon


title: GFP-LC3 oHSC_LO_23

description:
smartseq2
fcounts1.txt


title: 10uM_Diazinon_MCF7, M_316

description:
M_316
MCF7_Diazinon_10uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 10uM Diazinon


title: GFP-LC3 oHSC_MID_19

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_19

description:
smartseq2
fcounts1.txt


title: 207760740083_R08C01


title: 1mM_Diazinon_MCF7, M_315

description:
M_315
MCF7_Diazinon_1mM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740083_R06C01


title: GFP-LC3 oHSC_HI_18

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_18

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_18

description:
smartseq2
fcounts1.txt


title: 316uM_Diazinon_MCF7, M_314

description:
M_314
MCF7_Diazinon_316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740030_R12C01


title: 100uM_Diazinon_MCF7, M_313

description:
M_313
MCF7_Diazinon_100uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740030_R10C01


title: GFP-LC3 yHSC_18

description:
smartseq2
fcounts1.txt


title: 31.6uM_Diazinon_MCF7, M_312

description:
M_312
MCF7_Diazinon_31.6uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740083_R02C01


title: 10uM_Diazinon_MCF7, M_311

description:
M_311
MCF7_Diazinon_10uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_17

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_16

description:
smartseq2
fcounts1.txt


title: 1mM_Diazinon_MCF7, M_310

description:
M_310
MCF7_Diazinon_1mM_Rep2
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740056_R08C01


title: GFP-LC3 oHSC_LO_17

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_16

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_17

description:
smartseq2
fcounts1.txt


title: 207760740056_R04C01


title: 316uM_Diazinon_MCF7, M_309

description:
M_309
MCF7_Diazinon_316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740056_R06C01


title: GFP-LC3 yHSC_16

description:
smartseq2
fcounts1.txt


title: 207760740056_R02C01


title: 100uM_Diazinon_MCF7, M_308

description:
M_308
MCF7_Diazinon_100uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 31.6uM_Diazinon_MCF7, M_307

description:
M_307
MCF7_Diazinon_31.6uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740083_R04C01


title: GFP-LC3 oHSC_MID_15

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_17

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_15

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_15

description:
smartseq2
fcounts1.txt


title: 10uM_Diazinon_MCF7, M_306

description:
M_306
MCF7_Diazinon_10uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R06C01


title: GFP-LC3 oHSC_MID_16

description:
smartseq2
fcounts1.txt


title: 1mM_Diazinon_MCF7, M_305

description:
M_305
MCF7_Diazinon_1mM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R02C01


title: GFP-LC3 oHSC_MID_14

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_19

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_15

description:
smartseq2
fcounts1.txt


title: 207760740041_R04C01


title: GFP-LC3 oHSC_LO_14

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_14

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_13

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_13

description:
smartseq2
fcounts1.txt


title: 316uM_Diazinon_MCF7, M_304

description:
M_304
MCF7_Diazinon_316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740030_R08C01


title: GFP-LC3 oHSC_HI_12

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_13

description:
smartseq2
fcounts1.txt


title: 207760740030_R06C01


title: GFP-LC3 yHSC_13

description:
smartseq2
fcounts1.txt


title: 31.6uM_Diazinon_MCF7, M_302

description:
M_302
MCF7_Diazinon_31.6uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R08C01


title: GFP-LC3 oHSC_HI_14

description:
smartseq2
fcounts1.txt


title: 100uM_Diazinon_MCF7, M_303

description:
M_303
MCF7_Diazinon_100uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_LO_12

description:
smartseq2
fcounts1.txt


title: 10uM_Diazinon_MCF7, M_301

description:
M_301
MCF7_Diazinon_10uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 yHSC_12

description:
smartseq2
fcounts1.txt


title: 207760740030_R04C01


title: GFP-LC3 oHSC_MID_12

description:
smartseq2
fcounts1.txt


title: 3.16uM_Diazinon_MCF7, M_300

description:
M_300
MCF7_Diazinon_3.16uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 3.16uM Diazinon


title: GFP-LC3 oHSC_MID_11

description:
smartseq2
fcounts1.txt


title: 207760740083_R07C02


title: GFP-LC3 oHSC_LO_11

description:
smartseq2
fcounts1.txt


title: 207760740083_R05C02


title: GFP-LC3 oHSC_HI_10

description:
smartseq2
fcounts1.txt


title: 0.316uM_Diazinon_MCF7, M_298

description:
M_298
MCF7_Diazinon_0.316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.316uM Diazinon


title: GFP-LC3 yHSC_11

description:
smartseq2
fcounts1.txt


title: 207760740083_R03C02


title: GFP-LC3 yHSC_10

description:
smartseq2
fcounts1.txt


title: 0.1uM_Diazinon_MCF7, M_297

description:
M_297
MCF7_Diazinon_0.1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.1uM Diazinon


title: 207760740083_R01C02


title: GFP-LC3 oHSC_HI_9

description:
smartseq2
fcounts1.txt

value: bone marrow


title: 0uM_Diazinon_MCF7, M_296

description:
M_296
MCF7_Diazinon_0uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0uM Diazinon


title: 207760740056_R07C02


title: GFP-LC3 oHSC_LO_9

description:
smartseq2
fcounts1.txt

value: old


title: GFP-LC3 oHSC_MID_9

description:
smartseq2
fcounts1.txt

value: Haematopoietic stem cell


title: 3.16uM_Diazinon_MCF7, M_295

description:
M_295
MCF7_Diazinon_3.16uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740056_R05C02


title: 207760740030_R02C01


title: GFP-LC3 yHSC_9

description:
smartseq2
fcounts1.txt

value: steady state isolation


title: GFP-LC3 oHSC_HI_11

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_8

description:
smartseq2
fcounts1.txt


title: 1uM_Diazinon_MCF7, M_294

description:
M_294
MCF7_Diazinon_1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 1uM Diazinon


title: 207760740056_R03C02


title: GFP-LC3 oHSC_MID_8

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_8

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_8

description:
smartseq2
fcounts1.txt

value: young


title: 0.1uM_Diazinon_MCF7, M_292

description:
M_292
MCF7_Diazinon_0.1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_7

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_10

description:
smartseq2
fcounts1.txt


title: 0.316uM_Diazinon_MCF7, M_293

description:
M_293
MCF7_Diazinon_0.316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 1uM_Diazinon_MCF7, M_299

description:
M_299
MCF7_Diazinon_1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_LO_7

description:
smartseq2
fcounts1.txt


title: 207760740056_R01C02


title: GFP-LC3 oHSC_LO_10

description:
smartseq2
fcounts1.txt


title: 207760740041_R07C02


title: GFP-LC3 oHSC_MID_7

description:
smartseq2
fcounts1.txt


title: 0uM_Diazinon_MCF7, M_291

description:
M_291
MCF7_Diazinon_0uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R03C02


title: 207760740041_R05C02


title: GFP-LC3 oHSC_MID_6

description:
smartseq2
fcounts1.txt


title: 1uM_Diazinon_MCF7, M_289

description:
M_289
MCF7_Diazinon_1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_HI_6

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_LO_6

description:
smartseq2
fcounts1.txt


title: 3.16uM_Diazinon_MCF7, M_290

description:
M_290
MCF7_Diazinon_3.16uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R01C02


title: GFP-LC3 yHSC_6

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_5

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_5

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_MID_5

description:
smartseq2
fcounts1.txt


title: 207760740030_R05C02


title: 207760740030_R07C02


title: 0uM_Diazinon_MCF7, M_286

description:
M_286
MCF7_Diazinon_0uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0.1uM_Diazinon_MCF7, M_287

description:
M_287
MCF7_Diazinon_0.1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_LO_4

description:
smartseq2
fcounts1.txt


title: 0.316uM_Diazinon_MCF7, M_288

description:
M_288
MCF7_Diazinon_0.316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_4

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_4

description:
smartseq2
fcounts1.txt


title: 207760740083_R15C01

value: Jurkat


title: 207760740030_R01C02


title: 3.16uM_Diazinon_MCF7, M_285

description:
M_285
MCF7_Diazinon_3.16uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_MID_3

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_3

description:
smartseq2
fcounts1.txt


title: GFP-LC3 oHSC_HI_2

description:
smartseq2
fcounts1.txt


title: 207760740083_R13C01


title: GFP-LC3 oHSC_LO_3

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_3

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_7

description:
smartseq2
fcounts1.txt


title: 207760740030_R03C02


title: GFP-LC3 oHSC_LO_5

description:
smartseq2
fcounts1.txt


title: 0.316uM_Diazinon_MCF7, M_283

description:
M_283
MCF7_Diazinon_0.316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 yHSC_4

description:
smartseq2
fcounts1.txt


title: 207760740083_R11C01


title: 0uM_Diazinon_MCF7, M_281

description:
M_281
MCF7_Diazinon_0uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: GFP-LC3 oHSC_LO_2

description:
smartseq2
fcounts1.txt


title: GFP-LC3 yHSC_2

description:
smartseq2
fcounts1.txt


title: 0.1uM_Diazinon_MCF7, M_282

description:
M_282
MCF7_Diazinon_0.1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740083_R09C01


title: GFP-LC3 oHSC_HI_1

description:
smartseq2
fcounts1.txt


title: 10uM_Sulforaphane_MCF7, M_280

description:
M_280
MCF7_Sulforaphane_10uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 10uM Sulforaphane


title: GFP-LC3 oHSC_MID_1

description:
smartseq2
fcounts1.txt


title: 207760740056_R15C01


title: 3.16uM_Sulforaphane_MCF7, M_279

description:
M_279
MCF7_Sulforaphane_3.16uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell

value: MCF7 cells treated with 3.16uM Sulforaphane


title: GFP-LC3 oHSC_LO_1

description:
smartseq2
fcounts1.txt


title: 1uM_Diazinon_MCF7, M_284

description:
M_284
MCF7_Diazinon_1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740056_R13C01


title: GFP-LC3 yHSC_1

description:
smartseq2
fcounts1.txt


title: 1uM_Sulforaphane_MCF7, M_278

description:
M_278
MCF7_Sulforaphane_1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 1uM Sulforaphane


title: CTX Control 2

city: LOS ANGELES

first: Chia-ho

last: Lin

state: CA

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

description: Ribosome protected mRNA fragments

data_processing:
Sequence reads were demultiplexed using HtSeqTools.
Input sequence reads linkers and adapters were removed with cutadapt.
Reads shorter than 24nt were discarded. Reads were aligned to the mm10 rRNA sequences with bowtie with default parameters and unaligned reads were retained
Reads were then aligned to the mm10 genome using STAR 2.5.4b
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Cortex E15 DIV14

growth_protocol: E15 Rbfox1 fl/fl primary neuronal cultures were plated on PDLL coated 10cm plates at 5.8E+6 density. Plating media changed to feeding media after 24 hours and fed every 3-5 days thereafter.

extract_protocol:
Cells were harvested at DIV14. each plates was washed with ice-cold PBS containing 100ug CHX, lysed in dish with 400ul lysis buffer, scraped, left for 10minutes, and triturated 5x using a G26 needle.
Library was constructed following the protocol discribed by  Nicholas J. McGlincy and Nicholas T. Ingolia, Methods 2017. (titled: Transcriptome-wide measurement of translation by ribosome profiling)

treatment_protocol: AAV2/9-hSyn-Cre-eGFP or AAV2/9-hSyn-eGFP virus was used to infect cells at DIV3. Approximately 100% infection efficiency.

value: Cortex E15 DIV14

value: A0011 GGCTAC

value: NI-814 GATCA


title: CTX Control 1

description: Ribosome protected mRNA fragments

value: NI-813 CTAGA


title: 207760740056_R11C01


title: GFP-LC3 oHSC_MID_2

description:
smartseq2
fcounts1.txt


title: 0.316uM_Sulforaphane_MCF7, M_277

description:
M_277
MCF7_Sulforaphane_0.316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.316uM Sulforaphane


title: CTX Rbfox1 cKO 1

description: Ribosome protected mRNA fragments

value: A0010 TAGCTT

value: NI-810 ATCGT


title: 207760740056_R09C01


title: 0.1uM_Sulforaphane_MCF7, M_276

description:
M_276
MCF7_Sulforaphane_0.1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.1uM Sulforaphane


title: Placenta_Saline_M_repl8

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

description: 3' Quant seq with UMI tags

data_processing:
Raw sequencing reads were assessed for quality control using FastQC and multiqc umi indexes were added using umi2index (Lexogen) and then trimmed to remove adapter contamination, polyA read through and low-quality reads using BBDuk.
All samples were then re-assessed for quality using FastQC and multiqc.
Samples were aligned to the mouse genome (mm10) using STAR
Aligned bam files were then filtered for only unique UMIs using collapse_UMI_bam (Lexogen).
Filtered bam files were sorted and indexed using samtools.
Reads per gene were then counted using feature counts at the gene id levels with -s 1 desginated for stranded RNAseq.
Counts were then read into R for statistical analysis using EdgeR and LimmaVoom.
Assembly: mm10
Supplementary files format and content: FeatureCounts counts table in .txt

source_name: placenta

extract_protocol:
5 days following the Poly I:C injection on ED17.5, pregnant dams were euthanized using CO2. The uterine horn was dissected out and placenta and fetal brains were taken from each of the offspring and flash frozen with dry ice. RNA was isolated from fetal brain (n = 32; 16 males and 16 females) and placentas (n = 32; 16 males and 16 females) from 7-8 litters using RNA/DNA Miniprep Plus Zymogen Kit (Cat#D7003). To ensure purity, RNA was further treated with DNAse1 for 15 minutes. RNA quantification was done using a Qubit. Chemical purity was determined using a Nanodrop, where the absorbance ratios fell between 1.6 and 2.1(260/280) and above 1.3 (260/230). cDNA libraries were prepared according to the Lexogen manual, using 500ng of total input RNA per sample and 12 cycles of PCR amplification. 64 unique, dual index barcodes were used and samples were then pooled.
QuantSeq 3’mRNA sequencing FWD (RNAseq) libraries (Lexogen) were prepared as stated in the Lexogen manual using 500ng of total input RNA per sample and 12 cycles of PCR amplification. 64 unique, dual index barcodes were used and samples were then pooled. Unique molecular identifiers were used in place of SS1.
Pooled samples were exonuclease VII treated and sequenced on the HiSeq4000 to generate Single End 100 base pair reads.

treatment_protocol: 8–10 week-old female C576B/L mice were paired with males. Insemination was confirmed by the presence of a vaginal plug the following morning, marking the gestational time as embryonic day (ED) 0.5. On embryonic day 12.5, pregnant dams were intraperitoneally administered 20mg/kg γ-irradiated Poly I:C (Sigma) to stimulate maternal immune activation. Control groups were administered saline.

tag: litter

tag: uterine horn position

value: F

tag: Sex

value: Male

tag: embryo age in days of gestation

tag: treatment on ex

value: Saline

tag: strain


title: 207760740041_R15C01


title: Placenta_Saline_M_repl7

description: 3' Quant seq with UMI tags

value: D


title: Placenta_Saline_M_repl6

description: 3' Quant seq with UMI tags


title: 10uM_Sulforaphane_MCF7, M_275

description:
M_275
MCF7_Sulforaphane_10uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R13C01

value: Jurkat


title: Placenta_Saline_M_repl5

description: 3' Quant seq with UMI tags


title: Placenta_Saline_M_repl4

description: 3' Quant seq with UMI tags


title: 207760740041_R11C01


title: Placenta_Saline_M_repl3

description: 3' Quant seq with UMI tags


title: Placenta_Saline_M_repl2

description: 3' Quant seq with UMI tags


title: 207760740041_R09C01


title: 1uM_Sulforaphane_MCF7, M_273

description:
M_273
MCF7_Sulforaphane_1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 3.16uM_Sulforaphane_MCF7, M_274

description:
M_274
MCF7_Sulforaphane_3.16uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: Placenta_Saline_M_repl1

description: 3' Quant seq with UMI tags


title: Placenta_Saline_F_repl8

description: 3' Quant seq with UMI tags

value: C

value: Female


title: 207760740030_R15C01


title: Placenta_Saline_F_repl5

description: 3' Quant seq with UMI tags


title: Placenta_Saline_F_repl7

description: 3' Quant seq with UMI tags


title: 0.316uM_Sulforaphane_MCF7, M_272

description:
M_272
MCF7_Sulforaphane_0.316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell


title: Placenta_Saline_F_repl6

description: 3' Quant seq with UMI tags


title: 10uM_Sulforaphane_MCF7, M_270

description:
M_270
MCF7_Sulforaphane_10uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 10uM Sulforaphane


title: Placenta_Saline_F_repl3

description: 3' Quant seq with UMI tags

value: E


title: 0.1uM_Sulforaphane_MCF7, M_271

description:
M_271
MCF7_Sulforaphane_0.1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 3.16uM_Sulforaphane_MCF7, M_269

description:
M_269
MCF7_Sulforaphane_3.16uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 3.16uM Sulforaphane


title: Placenta_Poly IC_M_repl8

description: 3' Quant seq with UMI tags

value: Poly IC


title: 207760740030_R13C01


title: Placenta_Poly IC_M_repl7

description: 3' Quant seq with UMI tags


title: Placenta_Saline_F_repl4

description: 3' Quant seq with UMI tags


title: 207760740030_R09C01


title: Placenta_Poly IC_M_repl6

description: 3' Quant seq with UMI tags


title: Placenta_Saline_F_repl2

description: 3' Quant seq with UMI tags


title: Placenta_Poly IC_M_repl3

description: 3' Quant seq with UMI tags


title: 0.1uM_Sulforaphane_MCF7, M_266

description:
M_266
MCF7_Sulforaphane_0.1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740083_R03C01

value: Hela


title: 207760740083_R07C01


title: 1uM_Sulforaphane_MCF7, M_268

description:
M_268
MCF7_Sulforaphane_1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 1uM Sulforaphane


title: 0.316uM_Sulforaphane_MCF7, M_267

description:
M_267
MCF7_Sulforaphane_0.316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.316uM Sulforaphane


title: 207760740030_R11C01


title: Placenta_Poly IC_M_repl4

description: 3' Quant seq with UMI tags


title: Placenta_Poly IC_F_repl8

description: 3' Quant seq with UMI tags


title: Placenta_Poly IC_F_repl6

description: 3' Quant seq with UMI tags


title: Placenta_Poly IC_M_repl2

description: 3' Quant seq with UMI tags


title: Placenta_Poly IC_F_repl5

description: 3' Quant seq with UMI tags


title: 10uM_Sulforaphane_MCF7, M_265

description:
M_265
MCF7_Sulforaphane_10uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: Placenta_Poly IC_M_repl1

description: 3' Quant seq with UMI tags